LOCUS       NM_005506               4694 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens scavenger receptor class B member 2 (SCARB2),
            transcript variant 1, mRNA.
ACCESSION   NM_005506
VERSION     NM_005506.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 4694)
  AUTHORS   Zhang,D., Fang,J., Shan,J., Xu,L., Wu,Y., Lu,B., Zhang,X., Wang,C.,
            Sun,P. and Wang,Q.
  TITLE     SCARB2 associates with tumor-infiltrating neutrophils and predicts
            poor prognosis in breast cancer
  JOURNAL   Breast Cancer Res Treat 207 (1), 15-24 (2024)
   PUBMED   38914918
  REMARK    GeneRIF: SCARB2 associates with tumor-infiltrating neutrophils and
            predicts poor prognosis in breast cancer.
REFERENCE   2  (bases 1 to 4694)
  AUTHORS   Ecard,J., Lian,Y.L., Divoux,S., Gouveia,Z., Vigne,E., Perez,F. and
            Boncompain,G.
  TITLE     Lysosomal membrane proteins LAMP1 and LIMP2 are segregated in the
            Golgi apparatus independently of their clathrin adaptor binding
            motif
  JOURNAL   Mol Biol Cell 35 (3), ar42 (2024)
   PUBMED   38231876
  REMARK    GeneRIF: Lysosomal membrane proteins LAMP1 and LIMP2 are segregated
            in the Golgi apparatus independently of their clathrin adaptor
            binding motif.
REFERENCE   3  (bases 1 to 4694)
  AUTHORS   Nishimura,Y., Sato,K., Koyanagi,Y., Wakita,T., Muramatsu,M.,
            Shimizu,H., Bergelson,J.M. and Arita,M.
  TITLE     Enterovirus A71 does not meet the uncoating receptor SCARB2 at the
            cell surface
  JOURNAL   PLoS Pathog 20 (2), e1012022 (2024)
   PUBMED   38359079
  REMARK    GeneRIF: Enterovirus A71 does not meet the uncoating receptor
            SCARB2 at the cell surface.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 4694)
  AUTHORS   Tian,Y., Liang,L., Chen,J., Liu,J., Su,Y., Shi,M., Li,W., Zhang,J.,
            Feng,Y., He,L., Liu,H. and Yang,X.
  TITLE     Knockdown LIMP2 inhibits colorectal cancer cells migration,
            invasion, and metastasis
  JOURNAL   Exp Cell Res 431 (1), 113757 (2023)
   PUBMED   37640260
  REMARK    GeneRIF: Knockdown LIMP2 inhibits colorectal cancer cells
            migration, invasion, and metastasis.
REFERENCE   5  (bases 1 to 4694)
  AUTHORS   Wang,F., Gao,Y., Xue,S., Zhao,L., Jiang,H., Zhang,T., Li,Y.,
            Zhao,C., Wu,F., Siqin,T., Liu,Y., Wu,J., Yan,Y., Yuan,J.,
            Jiang,J.D. and Li,K.
  TITLE     SCARB2 drives hepatocellular carcinoma tumor initiating cells via
            enhanced MYC transcriptional activity
  JOURNAL   Nat Commun 14 (1), 5917 (2023)
   PUBMED   37739936
  REMARK    GeneRIF: SCARB2 drives hepatocellular carcinoma tumor initiating
            cells via enhanced MYC transcriptional activity.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 4694)
  AUTHORS   Crombie,R. and Silverstein,R.
  TITLE     Lysosomal integral membrane protein II binds thrombospondin-1.
            Structure-function homology with the cell adhesion molecule CD36
            defines a conserved recognition motif
  JOURNAL   J Biol Chem 273 (9), 4855-4863 (1998)
   PUBMED   9478926
REFERENCE   7  (bases 1 to 4694)
  AUTHORS   Calvo,D., Dopazo,J. and Vega,M.A.
  TITLE     The CD36, CLA-1 (CD36L1), and LIMPII (CD36L2) gene family: cellular
            distribution, chromosomal location, and genetic evolution
  JOURNAL   Genomics 25 (1), 100-106 (1995)
   PUBMED   7539776
REFERENCE   8  (bases 1 to 4694)
  AUTHORS   Sandoval,I.V., Arredondo,J.J., Alcalde,J., Gonzalez Noriega,A.,
            Vandekerckhove,J., Jimenez,M.A. and Rico,M.
  TITLE     The residues Leu(Ile)475-Ile(Leu, Val, Ala)476, contained in the
            extended carboxyl cytoplasmic tail, are critical for targeting of
            the resident lysosomal membrane protein LIMP II to lysosomes
  JOURNAL   J Biol Chem 269 (9), 6622-6631 (1994)
   PUBMED   7509809
REFERENCE   9  (bases 1 to 4694)
  AUTHORS   Xiao,C., Ahn,H., Kibrom,S. and Toro,C.
  TITLE     SCARB2-Related Action Myoclonus - Renal Failure Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   26677510
REFERENCE   10 (bases 1 to 4694)
  AUTHORS   Fujita,H., Takata,Y., Kono,A., Tanaka,Y., Takahashi,T., Himeno,M.
            and Kato,K.
  TITLE     Isolation and sequencing of a cDNA clone encoding the 85 kDa human
            lysosomal sialoglycoprotein (hLGP85) in human metastatic pancreas
            islet tumor cells
  JOURNAL   Biochem Biophys Res Commun 184 (2), 604-611 (1992)
   PUBMED   1374238
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC034139.7, AK313016.1,
            AC110795.4 and BC035111.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_005506.3.
            
            Summary: The protein encoded by this gene is a type III
            glycoprotein that is located primarily in limiting membranes of
            lysosomes and endosomes. Earlier studies in mice and rat suggested
            that this protein may participate in membrane transportation and
            the reorganization of endosomal/lysosomal compartment. The protein
            deficiency in mice was reported to impair cell membrane transport
            processes and cause pelvic junction obstruction, deafness, and
            peripheral neuropathy. Further studies in human showed that this
            protein is a ubiquitously expressed protein and that it is involved
            in the pathogenesis of HFMD (hand, foot, and mouth disease) caused
            by enterovirus-71 and possibly by coxsackievirus A16. Mutations in
            this gene caused an autosomal recessive progressive myoclonic
            epilepsy-4 (EPM4), also known as action myoclonus-renal failure
            syndrome (AMRF). Alternatively spliced transcript variants encoding
            different isoforms have been found for this gene.[provided by
            RefSeq, Feb 2011].
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (1).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803613.98024.1,
                                           SRR1660809.148205.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2467146 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000264896.8/ ENSP00000264896.2
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-215               AC034139.7         790-1004            c
            216-1718            AK313016.1         1-1503
            1719-4527           AC110795.4         19380-22188         c
            4528-4694           BC035111.1         1349-1515
FEATURES             Location/Qualifiers
     source          1..4694
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="4"
                     /map="4q21.1"
     gene            1..4694
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /note="scavenger receptor class B member 2"
                     /db_xref="GeneID:950"
                     /db_xref="HGNC:HGNC:1665"
                     /db_xref="MIM:602257"
     exon            1..398
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     CDS             282..1718
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /note="isoform 1 is encoded by transcript variant 1; CD36
                     antigen (collagen type I receptor, thrombospondin
                     receptor)-like 2 (lysosomal integral membrane protein II);
                     85 kDa lysosomal sialoglycoprotein scavenger receptor
                     class B, member 2; lysosome membrane protein 2; LIMP II;
                     CD36 antigen-like 2; lysosome membrane protein II; 85 kDa
                     lysosomal membrane sialoglycoprotein"
                     /codon_start=1
                     /product="lysosome membrane protein 2 isoform 1"
                     /protein_id="NP_005497.1"
                     /db_xref="CCDS:CCDS3577.1"
                     /db_xref="GeneID:950"
                     /db_xref="HGNC:HGNC:1665"
                     /db_xref="MIM:602257"
                     /translation="MGRCCFYTAGTLSLLLLVTSVTLLVARVFQKAVDQSIEKKIVLR
                     NGTEAFDSWEKPPLPVYTQFYFFNVTNPEEILRGETPRVEEVGPYTYRELRNKANIQF
                     GDNGTTISAVSNKAYVFERDQSVGDPKIDLIRTLNIPVLTVIEWSQVHFLREIIEAML
                     KAYQQKLFVTHTVDELLWGYKDEILSLIHVFRPDISPYFGLFYEKNGTNDGDYVFLTG
                     EDSYLNFTKIVEWNGKTSLDWWITDKCNMINGTDGDSFHPLITKDEVLYVFPSDFCRS
                     VYITFSDYESVQGLPAFRYKVPAEILANTSDNAGFCIPEGNCLGSGVLNVSICKNGAP
                     IIMSFPHFYQADERFVSAIEGMHPNQEDHETFVDINPLTGIILKAAKRFQINIYVKKL
                     DDFVETGDIRTMVFPVMYLNESVHIDKETASRLKSMINTTLIITNIPYIIMALGVFFG
                     LVFTWLACKGQGSMDEGTADERAPLIRT"
     exon            399..556
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            557..704
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            705..893
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            894..985
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            986..1105
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            1106..1275
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            1276..1394
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            1395..1468
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            1469..1520
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            1521..1679
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     exon            1680..4694
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1960..1965
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /note="hexamer: AATAAA"
     polyA_site      1979
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
     regulatory      4671..4676
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /note="hexamer: AATAAA"
     polyA_site      4694
                     /gene="SCARB2"
                     /gene_synonym="AMRF; CD36L2; EPM4; HLGP85; LGP85; LIMP-2;
                     LIMPII; SR-BII"
                     /note="major polyA site"
ORIGIN      
        1 actctcccga gctgcgctag gcgggcgcca cggctgcccg gcgaaggaaa ccgaaaccga
       61 gtccgggccc gtccctccgc ggccccatcc gcccggtgca cccggggccg cgctcgccag
      121 gccgcggagc ccagagctgc gcgcacgaac cgtgcgccgg gagggcgtgg gcgtggcgcc
      181 gaagggtccc gggtcttcga cgcctctgcg gcggctcctc cctccttgca gttggatccc
      241 tggcgggtgc ggcccggccc ggcccgtgag cggcgcacag aatgggccga tgctgcttct
      301 acacggcggg gacgttgtcc ctgctcctgc tggtgaccag cgtcacgctg ctggtggccc
      361 gggtcttcca gaaggctgta gaccagagta tcgagaagaa aattgtgtta aggaatggta
      421 ctgaggcatt tgactcctgg gagaagcccc ctctgcctgt gtatactcag ttctatttct
      481 tcaatgtcac caatccagag gagatcctca gaggggagac ccctcgggtg gaagaagtgg
      541 ggccatacac ctacagggaa ctcagaaaca aagcaaatat tcaatttgga gataatggaa
      601 caacaatatc tgctgttagc aacaaggcct atgtttttga acgagaccaa tctgttggag
      661 accctaaaat tgacttaatt agaacattaa atattcctgt attgactgtc atagagtggt
      721 cccaggtgca cttcctcagg gagatcatcg aggccatgtt gaaagcctat cagcagaagc
      781 tctttgtgac tcacacagtt gacgaattgc tctggggcta caaagatgaa atcttgtccc
      841 ttatccatgt tttcaggccc gatatctctc cctattttgg cctattctat gagaaaaatg
      901 ggactaatga tggagactat gtttttctaa ctggagaaga cagttacctt aactttacaa
      961 aaattgtgga atggaatggg aaaacgtcac ttgactggtg gataacagac aagtgcaata
     1021 tgattaatgg aacagatgga gattcttttc acccactaat aaccaaagat gaggtccttt
     1081 atgtcttccc atctgacttt tgcaggtcag tgtatattac tttcagtgac tatgagagtg
     1141 tacagggact gcctgccttt cggtataaag ttcctgcaga aatattagcc aatacgtcag
     1201 acaatgccgg cttctgtata cctgagggaa actgcctggg ctcaggagtt ctgaatgtca
     1261 gcatctgcaa gaatggtgca cccatcatta tgtctttccc acacttttac caagcagatg
     1321 agaggtttgt ttctgccata gaaggcatgc acccaaatca ggaagaccat gagacatttg
     1381 tggacattaa tcctttgact ggaataatcc taaaagcagc caagaggttc caaatcaaca
     1441 tttatgtcaa aaaattagat gactttgttg aaacgggaga cattagaacc atggttttcc
     1501 cagtgatgta cctcaatgag agtgttcaca ttgataaaga gacggcgagt cgactgaagt
     1561 ctatgattaa cactactttg atcatcacca acatacccta catcatcatg gcgctgggtg
     1621 tgttctttgg tttggttttt acctggcttg catgcaaagg acagggatcc atggatgagg
     1681 gaacagcgga tgaaagagca cccctcattc gaacctaaac attgcctttg cttggtgaag
     1741 aaactgtgtg agctgtcctg acctggacga tgacgtgggg aaaccctcca cctccttgca
     1801 ggcttgttgc ctgttgaaag aaggaaaaag acacggcgct ggcaagtgat aggaacattc
     1861 tggccagagg ttaaagagca ggctgacatg gctggccatt aagctttata aaatcatgtg
     1921 ggctctgaaa ttgttctttt atgtgtctag caagtattta ataaaccctt gtatagtaat
     1981 tttgttgttg ttgggtgctg gtagctccag aattttgtga ccactattgt gggtaaaatg
     2041 tctctgcatc acttgttaat gctactggtc taacttcatt cagtatgctt cattcaccga
     2101 actttgtgct caaaatgcgt atataccatt ttatgttgta ttcctccatt tcacttgcaa
     2161 aacagaagta aataagagtt cgggacccag ggtaaaatgg tagcttcatc caatatatca
     2221 ttcaaatgca tctgatttct aaaacatatt acattttatg ctgatcttca gttcataatt
     2281 cttccaggaa aactcagtct tccaactgca ataaaatact gggtagaatc aaatgggaaa
     2341 ggggttgggt ggggcaatac ccatgagttg atagtgataa gctcctaagg atttttaact
     2401 tgtacttttg tgaacgaaga gaatgcataa ataatgttgg tgaggataaa gtacagatat
     2461 ttcatgtaga attaattgct agttatgatg cttgtggata gttaactgtt ttttttttag
     2521 tcaaaatgat catgctacga aaagatgctt ctgagagaat gtaatgagta actgattttt
     2581 cttcctgagt cgcccttgcc aaatatgtta ctgtattaat taatctaata ttgagtgatt
     2641 atttgtaaaa ttatgaatat gggaaatcca tctatctaca gcctaagtta cacataagtt
     2701 tcagaaagtc tgattagact aaagagatat ttcttctggg acagccgcct tcttggtaat
     2761 tttgaagttc tttttacaag ttccttcctc agtttcagtt ctttccagtg ttttgtagct
     2821 cactgtcact cactgaatag agaaacgtgt gccctatact tcctgtgaca atcattttgc
     2881 tgacagaatg atggatgttt aaaatattgc acaaagtact ttaaagaaag gtctgttagg
     2941 accagaagca gagacaccac ttttcaaagg acttcttggt ttcagcataa cctaagacag
     3001 ggaattggga gccatcatat gtcacagtgt tcagaattca agcatattta agggcatttt
     3061 ctttgattct caaagttcag cattcatttt gaattgagaa gcctatacat ttagctgaca
     3121 aagtgcttat agaatttctt aacaactgaa ccattcaaaa ggattttttt tgtttaaaac
     3181 tggatttcaa tgtaagcaaa tgaagaaaaa aatatagatt tcatttccat agcttcttat
     3241 ccctgtattg aggtaataaa ttgttttact gacaattttt cctttttcta cactaaaaca
     3301 atatgtgata tatttcccct cttgaagagg caattcatta aactctcaaa ttttctatag
     3361 aatcaagata gaacctttag atactccaac tcaccaaaat gtaaaaaaac taacaaaaat
     3421 atttggtctt caataatgct aaatatctac atttttagaa tttatcaaca tttaactaga
     3481 taattgggca tgtcttaatt atgcatgtac ttatccatac taataaaatt gacaatgcta
     3541 gtgcatactt attggtttag tcctattatc aggatataat catctgtgag gaggatattt
     3601 taaatactgt aaatgataac agttaatgat atacacattt agactgagtt gcacactggc
     3661 agggagacca aaaacattac ttccatactt gtgtcatgat tctttttttt ttgagagagt
     3721 ctcactctgt cgccaggctg gagtacagtg gcatgatctc ggctcactgc aacctctgcc
     3781 tcccgggttc aagcaattct cctgcctcag ccacccaagt agctgggact acaggtgcgt
     3841 gccaccacgc ccagctaaat tttgtatttt tagtggagac ggggtttcac catgttggcc
     3901 aggatggtct caatctcctg accctgcgat ctgcccacct cagcctccca aagtgctggg
     3961 attacaggcg taagccaccg ggcctggcct gttttatgat tcttaatagt tacttggttt
     4021 aaatcacatt tgatactatc cttctgaaaa gtctgagaca gatctacaaa ctacagtcaa
     4081 aattatagat taagaggaat gaatgcacct atttggcttt aagttgaaga tgaattattt
     4141 ctcatgctca ttttcttgcg gcagttatct tagaaagacc cccaaaggct ttgtgattgt
     4201 aagcactgtc atgatcacag aatgcaagct tctggtacca tgatcctcaa cttagagagg
     4261 aagaaaccaa gacagagagc ttaactcact tctctcaggg aaaattagga gttgagcaca
     4321 ggacaggaaa tgggctttgc cacttttagc tccaggcttt tctaaccaga cttgatttcc
     4381 tcatgttcta gaaagatcac taatggtcaa gtggaacaag cactacacga ctaaccccta
     4441 ttggggtttt taacttaagg gaggctaatt tttaatttaa actgctcgag atatgagttc
     4501 tgcaaaaggt ggtccgcatc cttggccctc tggacattat cactaaattg cttgtgcctg
     4561 ttaacaagaa tactgaccag aatgctcttc atgtagctta tacagttggt tcacttcatg
     4621 cggttcttga catgtttatt tctaccctta atgcaatgaa atgtttcatt aataaaaaac
     4681 cactttatat aaaa
//
